Map impacts for all impacted species

library(raster)
source('https://raw.githubusercontent.com/oharac/src/master/R/common.R')

source(here('common_fxns.R'))

library(animation)

reload <- FALSE

1 Summary

Create a species richness map for threatened marine species.

Combine taxa-level impact maps to create maps of number of threatened species impacted per cell, per year.

Plot maps as animated rasters, both by absolute numbers of species impacted in a location and by proportion of species (impact counts / species richness).

This is all done at the level of cumulative impact category, not individual stressors.

2 Methods

2.1 Create species richness map for this assessment

Set up the dataframe of species to include. By taxon, load all species range maps, smash down to taxon-level species richness; then combine these for a total species richness.

2.2 Setup for mapping across all taxa

For each combination of climate/no climate and impacts/refugia:

• gather all taxa-level map files into a raster stack
• collapse the stack using calc(fun = sum, na.rm = TRUE)
• animate over the years

2.3 Create impact map for all included spp, by stressor category

2.3.1 maps by count of threatened species impacted

2.3.2 maps by percent of threatened species impacted

2.3.3 Compare prioritized count vs simple count

Just showing year 2013.